In [1]:
"""
Created on Sat Mar 30 07:59:28 2024
@author: marik
""";
In [2]:
import sys
sys.path.append('..')
import pandas as pd
import tomotree as tomo
import matplotlib.pyplot as plt
import numpy as np
Read the data¶
In [3]:
# csv_tof = 'tomoWood_data/3_TOFDefEcc.txt'
# csv_nodes = 'tomoWood_data/3_posRecDefEcc.txt'
csv_tof = 'tomoWood_data/1_TOFHealthy.txt'
csv_nodes = 'tomoWood_data/1_posRecHealthy.txt'
image_name = "tomoWood_data/1_PhotoHealthy.png"
scale = 2.8
shift = np.array([350,300])
df = pd.read_csv(csv_nodes, sep='\t',header=None)
df = df.values*1000
nodes = df.copy()
nodes = nodes - nodes.mean(axis=0)
n2 = nodes.copy() # for aligning to image
n2[:,1] = -n2[:,1]
n2 = n2*scale + shift
im = plt.imread(image_name)
plt.imshow(im,zorder=1)
plt.scatter(*n2.T, s=np.arange(1,17)*5)
plt.title("Node positions. The size of the node corresponds to the node number.")
plt.gca().set_aspect(1);
In [4]:
df = pd.read_csv(csv_tof, sep='\t',header=None)
df.columns.name = "source node number"
df.columns = range(1,len(df.columns)+1)
df.index = range(1,len(df.index)+1)
plt.imshow(df.values.astype(float), cmap='Greys',
origin='lower')
plt.gca().set_aspect(0.5)
d = tomo.roll_table(df.values)*1000
In [5]:
df.plot(subplots=[np.arange(1,9),np.arange(9,17)])
# plt.plot(*nodes.T,'o')
Out[5]:
array([<Axes: >, <Axes: >], dtype=object)
In [6]:
t=tomo.Tomo(nodes=nodes, times=d.values, nx=31, ny=31)
t.plot(speed_min=1400, speed_max=1600, rays=False)
plt.suptitle("Speed as a mean value of ray speeds")
Out[6]:
Text(0.5, 0.98, 'Speed as a mean value of ray speeds')
In [7]:
speeds = t.speeds
speeds.style.highlight_max().format(precision=0).highlight_min(color='red')
Out[7]:
| Source node | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Receiver node | ||||||||||||||||
| 1 | nan | 1450 | 1456 | 1735 | 1487 | 1673 | 1562 | 1549 | 1473 | 1384 | 1509 | 1427 | 1628 | 1463 | 1304 | 2549 |
| 2 | 3150 | nan | 1369 | 1400 | 1462 | 1517 | 1387 | 1521 | 1537 | 1431 | 1491 | 1436 | 1545 | 1562 | 1434 | 1569 |
| 3 | 1428 | 1706 | nan | 1203 | 1412 | 1486 | 1601 | 1409 | 1503 | 1535 | 1421 | 1436 | 1598 | 1614 | 1508 | 1449 |
| 4 | 1530 | 1800 | 1390 | nan | 1263 | 1312 | 1317 | 1380 | 1573 | 1564 | 1569 | 1390 | 1566 | 1716 | 1671 | 1654 |
| 5 | 1353 | 1411 | 1791 | 1405 | nan | 1345 | 1153 | 2177 | 1673 | 1611 | 1449 | 1526 | 1592 | 1830 | 1720 | 1644 |
| 6 | 1460 | 1502 | 1477 | 1471 | 1140 | nan | 1515 | 1360 | 1589 | 1619 | 1629 | 1539 | 1530 | 1697 | 1720 | 1686 |
| 7 | 1336 | 1347 | 1390 | 1444 | 1320 | 1138 | nan | 3686 | 2154 | 1775 | 1599 | 1533 | 1572 | 1589 | 1671 | 1686 |
| 8 | 1553 | 1338 | 1337 | 1579 | 1590 | 1324 | 1401 | nan | 2228 | 1844 | 1618 | 1642 | 1463 | 1579 | 1482 | 1677 |
| 9 | 1473 | 1435 | 1402 | 1635 | 1545 | 1681 | 1539 | 1919 | nan | 1256 | 1723 | 1436 | 1284 | 1489 | 1529 | 1498 |
| 10 | 1432 | 1431 | 1352 | 1505 | 1673 | 1620 | 1753 | 1424 | 3522 | nan | 1452 | 1403 | 1391 | 1547 | 1649 | 1613 |
| 11 | 1583 | 1455 | 1421 | 1482 | 1636 | 1840 | 1614 | 1541 | 1259 | 1994 | nan | 1411 | 1330 | 1540 | 1535 | 1707 |
| 12 | 1676 | 1487 | 1441 | 1390 | 1605 | 1717 | 1737 | 1570 | 1565 | 1462 | 1400 | nan | 1466 | 1585 | 1387 | 1737 |
| 13 | 1503 | 1620 | 1477 | 1580 | 1592 | 1563 | 1694 | 1525 | 1411 | 1396 | 1983 | 1323 | nan | 1324 | 1430 | 1613 |
| 14 | 1497 | 1563 | 1491 | 1541 | 1559 | 1697 | 1571 | 1563 | 1517 | 1562 | 2409 | 1810 | 1504 | nan | 2459 | 1821 |
| 15 | 1761 | 1700 | 1522 | 1578 | 1648 | 1591 | 1671 | 1520 | 1464 | 1432 | 1768 | 1528 | 1742 | 1463 | nan | 3262 |
| 16 | 1687 | 1551 | 1669 | 1582 | 1564 | 1551 | 1760 | 1677 | 1486 | 1477 | 1704 | 1517 | 1774 | 1396 | 1277 | nan |
In [8]:
diff = (speeds - speeds.T)/2
diff.style.highlight_max().format(precision=0).highlight_min(color='red')
Out[8]:
| Source node | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Receiver node | ||||||||||||||||
| 1 | nan | -850 | 14 | 102 | 67 | 106 | 113 | -2 | 0 | -24 | -37 | -124 | 63 | -17 | -229 | 431 |
| 2 | 850 | nan | -169 | -200 | 25 | 7 | 20 | 92 | 51 | 0 | 18 | -26 | -38 | -1 | -133 | 9 |
| 3 | -14 | 169 | nan | -93 | -189 | 4 | 105 | 36 | 50 | 92 | 0 | -3 | 60 | 61 | -7 | -110 |
| 4 | -102 | 200 | 93 | nan | -71 | -80 | -64 | -100 | -31 | 29 | 44 | 0 | -7 | 87 | 47 | 36 |
| 5 | -67 | -25 | 189 | 71 | nan | 102 | -83 | 294 | 64 | -31 | -93 | -39 | 0 | 135 | 36 | 40 |
| 6 | -106 | -7 | -4 | 80 | -102 | nan | 188 | 18 | -46 | -1 | -105 | -89 | -17 | 0 | 65 | 67 |
| 7 | -113 | -20 | -105 | 64 | 83 | -188 | nan | 1142 | 307 | 11 | -8 | -102 | -61 | 9 | 0 | -37 |
| 8 | 2 | -92 | -36 | 100 | -294 | -18 | -1142 | nan | 154 | 210 | 39 | 36 | -31 | 8 | -19 | 0 |
| 9 | 0 | -51 | -50 | 31 | -64 | 46 | -307 | -154 | nan | -1133 | 232 | -65 | -64 | -14 | 33 | 6 |
| 10 | 24 | 0 | -92 | -29 | 31 | 1 | -11 | -210 | 1133 | nan | -271 | -29 | -3 | -7 | 109 | 68 |
| 11 | 37 | -18 | 0 | -44 | 93 | 105 | 8 | -39 | -232 | 271 | nan | 6 | -326 | -434 | -116 | 1 |
| 12 | 124 | 26 | 3 | 0 | 39 | 89 | 102 | -36 | 65 | 29 | -6 | nan | 71 | -112 | -70 | 110 |
| 13 | -63 | 38 | -60 | 7 | 0 | 17 | 61 | 31 | 64 | 3 | 326 | -71 | nan | -90 | -156 | -80 |
| 14 | 17 | 1 | -61 | -87 | -135 | 0 | -9 | -8 | 14 | 7 | 434 | 112 | 90 | nan | 498 | 213 |
| 15 | 229 | 133 | 7 | -47 | -36 | -65 | 0 | 19 | -33 | -109 | 116 | 70 | 156 | -498 | nan | 992 |
| 16 | -431 | -9 | 110 | -36 | -40 | -67 | 37 | 0 | -6 | -68 | -1 | -110 | 80 | -213 | -992 | nan |
In [9]:
t.check_triangle_inequality()
Out[9]:
'Triangle inequality failed 98 out of 3360 which is 3%.'
In [10]:
ax = t.plot_angular_dependence()
ax.set(ylim=(None,2000))
Out[10]:
[(1010.6944579547201, 2000.0)]
EBSI method¶
In [11]:
t1=tomo.Tomo(nodes=nodes, times=d.values,nx=61,ny=61)
t1.do_EBSI_method()
Out[11]:
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In [12]:
limits = t1.limit_cell_plot_velocities(4)
t1.plot(rays=False, **limits)
Out[12]:
<Axes: >
SIRT method¶
In [13]:
t2=tomo.Tomo(nodes=nodes, times=d.values, nx=31, ny=31)
t2.do_SIRT_method(speed_min=800, speed_max=1800)
Out[13]:
'SIRT finished in 513 ms.\nSpeed interval: min=800.0 for 10 segments, max=1800.0 for 2016 segments'
In [14]:
t2.plot(speed_min=800, speed_max=1800)
plt.suptitle("SIRT method")
Out[14]:
Text(0.5, 0.98, 'SIRT method')
ERSM method with tangential velocities fixed¶
In [15]:
t3=tomo.Tomo(nodes=nodes, times=d.values, nx=51, ny=51, symmetric=True)
t3.do_ERSM_method()
In [16]:
limits = t3.limit_cell_plot_velocities(4)
t3.plot(grid=True, rays=False, **limits)
plt.suptitle("ERSM method with fixed tangential velocity")
Out[16]:
Text(0.5, 0.98, 'ERSM method with fixed tangential velocity')
ERSM method¶
Do not fix nonradial velocity
In [17]:
t4=tomo.Tomo(nodes=nodes, times=d.values, nx=51, ny=51, symmetric=True)
t4.do_ERSM_method(fix_velocity_EBSI_function=lambda x, y: x )
In [18]:
t4.plot(speed_min=1400, speed_max=1600)
Out[18]:
<Axes: >
In [19]:
limits = t4.limit_cell_plot_velocities(4)
t4.plot(rays=False, **limits)
plt.suptitle("ERSM method, tangential velocity not fixed")
Out[19]:
Text(0.5, 0.98, 'ERSM method, tangential velocity not fixed')
In [ ]:
In [ ]: